CNVRuler

A user-friendly program for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification.

Publication for CNVRuler

CNVRuler citations

A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits

2017

PLoS One

PMCID: 5417718

PMID: 28472114

DOI: 10.1371/journal.pone.0177014

[…] .The CNVRs were determined by merging CNVs identified in two or more animals when the overlap is of at least 1 bp, according to the criteria proposed by Redon et al. []. This merging was performed by CNVRuler software []. Regions of very low density of overlapping (recurrence parameter<0.1) were not used in the analyses for a more robust definition of the beginning and end regions. […]

library_books

Genome Wide Detection of CNVs and Their Association with Meat Tenderness in Nelore Cattle

Identification of Copy Number Variations in Xiang and Kele Pigs

2016

PLoS One

PMCID: 4740446

PMID: 26840413

DOI: 10.1371/journal.pone.0148565

[…] s because the samples were obtained from multiple locations across Congjiang County, China. Thus, pedigree information was not incorporated into the analysis. Moreover, the CNVs were aggregated using CNVRuler software []. […]

library_books

Identification of rare germline copy number variations over represented in five human cancer types

2015

Mol Cancer

PMCID: 4381456

PMID: 25644941

DOI: 10.1186/s12943-015-0292-6

[…] Illustrative examples of germline CNVRs are shown in Figure with the remaining CNVRs (in Table ) illustrated in (Additional file : Figure S1). CNVRuler (v1.3) was used to merge individual CNVs into common CNV regions (CNVR) for each cancer and control set []. CNVRs that did not have a recurrence of > 0.1 were filtered from the list. CNVR fre […]